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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ), 'gf_id' => 'HOM05D001204', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001204' ), 'data_identifier' => 'HOM05D001204', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001204', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '518', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p18940' => 'bna', 'A04p02530' => 'bna', 'A05p04490' => 'bna', 'A06p00300' => 'bna', 'A06p14480' => 'bna', 'A07p24190' => 'bna', 'A07p39740' => 'bna', 'A08p00770' => 'bna', 'Aa31LG10G1030' => 'aar', 'Aa31LG10G13120' => 'aar', 'Aa31LG1G25910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1844' => 'aag', 'Actinidia05840' => 'ach', 'Actinidia16264' => 'ach', 'Actinidia20334' => 'ach', 'Actinidia24459' => 'ach', 'Actinidia31715' => 'ach', 'Actinidia32410' => 'ach', 'Actinidia39825' => 'ach', 'Ah.11g045040' => 'amhyb', 'AL1G30840' => 'aly', 'AL1G63300' => 'aly', 'AL2G33730' => 'aly', 'AL4G43250' => 'aly', 'AL4G43260' => 'aly', 'AL5G40310' => 'aly', 'Aqoxy1G00069' => 'aox', 'Aqoxy279s003' => 'aox', 'Aqoxy279s004' => 'aox', 'Aqoxy2G00049' => 'aox', 'Aqoxy2G00050' => 'aox', 'Aqoxy3G00324' => 'aox', 'Aqoxy3G03948' => 'aox', 'Aqoxy7G01854' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2M9SF1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6K70BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8P2GFH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9UY3NV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9Z6I10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6LPEP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS2B16' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q1PQJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SDL2DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UA31PZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL8YIT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSXS9S' => 'arhy', 'AT1G55260' => 'ath', 'AT1G73890' => 'ath', 'AT2G44290' => 'ath', 'AT2G44300' => 'ath', 'AT3G58550' => 'ath', 'ATR0037G020' => 'atr', 'ATR0561G149' => 'atr', 'ATR0654G001' => 'atr', 'ATR0654G004' => 'atr', 'ATR0654G005' => 'atr', 'ATR0654G006' => 'atr', 'ATR0665G088' => 'atr', 'ATR0665G631' => 'atr', 'ATR0681G111' => 'atr', 'ATR0684G104' => 'atr', 'ATR0684G126' => 'atr', 'ATR0829G011' => 'atr', 'ATR0979G001' => 'atr', 'ATR1082G001' => 'atr', 'Atru.chr11.2713' => 'acertr', 'Atru.chr3.2271' => 'acertr', 'Atru.chr9.820' => 'acertr', 'AUR62000022' => 'cqu', 'AUR62015312' => 'cqu', 'AUR62019193' => 'cqu', 'AUR62025856' => 'cqu', 'AUR62029857' => 'cqu', 'AUR62032750' => 'cqu', 'BcaB02g08258' => 'bca', 'BcaB02g08808' => 'bca', 'BcaB07g31850' => 'bca', 'BcaC02g10015' => 'bca', 'BcaC07g41331' => 'bca', 'BcaC08g44923' => 'bca', 'BcaNung06604' => 'bca', 'BolC2t09179H' => 'bol', 'BolC3t21570H' => 'bol', 'BolC4t22160H' => 'bol', 'BolC4t24962H' => 'bol', 'BolC5t30369H' => 'bol', 'BolC6t36096H' => 'bol', 'BolC6t37711H' => 'bol', 'BolC6t39838H' => 'bol', 'BraA02t06936Z' => 'bra', 'BraA04t15981Z' => 'bra', 'BraA05t19425Z' => 'bra', 'BraA06t23247Z' => 'bra', 'BraA06t24572Z' => 'bra', 'BraA07t30062Z' => 'bra', 'BraA07t31523Z' => 'bra', 'BraA08t32134Z' => 'bra', 'C02p31480' => 'bna', 'C03p92560' => 'bna', 'C04p05200' => 'bna', 'C04p33950' => 'bna', 'C05p16700' => 'bna', 'C06p10220' => 'bna', 'C06p25490' => 'bna', 'C06p48030' => 'bna', 'CAN.G1361.2' => 'can', 'CAN.G1361.3' => 'can', 'CAN.G158.7' => 'can', 'CAN.G423.11' => 'can', 'CAN.G438.132' => 'can', 'CANSAT11G0424' => 'cansat', 'CANSAT11G0737' => 'cansat', 'CANSAT11G2194' => 'cansat', 'CANSAT80G0250' => 'cansat', 'CARHR019030' => 'chi', 'CARHR044910' => 'chi', 'CARHR067010' => 'chi', 'CARHR139470' => 'chi', 'CARHR168940' => 'chi', 'Carub.0001s4376' => 'cru', 'Carub.0002s2067' => 'cru', 'Carub.0004s2688' => 'cru', 'Carub.0004s2689' => 'cru', 'Carub.0005s2530' => 'cru', 'Ca_16389_v3' => 'car', 'Ca_17959_v3' => 'car', 'Ca_17961_v3' => 'car', 'Ca_26079_v3' => 'car', 'Ca_29697_v3' => 'car', 'Cc01_g02420' => 'ccan', 'Cc02_g26830' => 'ccan', 'Cc04_g07220' => 'ccan', 'Cc06_g09270' => 'ccan', 'Cc06_g15620' => 'ccan', 'CDE05G0269' => 'cde', 'CDE10G0509' => 'cde', 'Cfa009610' => 'cfa', 'Cfa010703' => 'cfa', 'Ciclev10010697m.g' => 'ccl', 'Ciclev10013719m.g' => 'ccl', 'Ciclev10016842m.g' => 'ccl', 'Ciclev10022419m.g' => 'ccl', 'Ciclev10033694m.g' => 'ccl', 'CiPaw.13G000500' => 'cil', 'CiPaw.13G174200' => 'cil', 'CiPaw.14G134000' => 'cil', 'CiPaw.15G129400' => 'cil', 'CiPaw.16G085700' => 'cil', 'ClCG02G023920' => 'cla', 'ClCG03G014040' => 'cla', 'ClCG06G014900' => 'cla', 'ClCG09G003660' => 'cla', 'COL.COLO4_04671' => 'col', 'COL.COLO4_16508' => 'col', 'COL.COLO4_29389' => 'col', 'COL.COLO4_34943' => 'col', 'COL.COLO4_34994' => 'col', 'Cpa.g.sc13.4' => 'cpa', 'Cpa.g.sc1500.3' => 'cpa', 'Cpa.g.sc23.158' => 'cpa', 'CsaV3_1G003760' => 'csa', 'CsaV3_1G042180' => 'csa', 'CsaV3_4G023430' => 'csa', 'CSS0003010' => 'camsi', 'CSS0029255' => 'camsi', 'CSS0036980' => 'camsi', 'CSS0037122' => 'camsi', 'DCAR_001989' => 'dca', 'DCAR_023200' => 'dca', 'DCAR_028738' => 'dca', 'Dinv09754' => 'din', 'Dinv09806' => 'din', 'Dinv13432' => 'din', 'Dinv28088' => 'din', 'Dinv41568' => 'din', 'Dinv43502' => 'din', 'Duzib068G0900' => 'dzi', 'Duzib128G1140' => 'dzi', 'Duzib150G0062' => 'dzi', 'Duzib168G0453' => 'dzi', 'Duzib170G0323' => 'dzi', 'Duzib205G2020' => 'dzi', 'Duzib268G0191' => 'dzi', 'ECA233G1648' => 'eca', 'ECA236G5040' => 'eca', 'ECA238G0462' => 'eca', 'EL10Ac3g06864' => 'bvu', 'EL10Ac4g10353' => 'bvu', 'EL10Ac5g11433' => 'bvu', 'Eucgr.B00719' => 'egr', 'Eucgr.B03623' => 'egr', 'Eucgr.B03624' => 'egr', 'Eucgr.H00429' => 'egr', 'FAN01G0173' => 'fan', 'FAN04G3054' => 'fan', 'FAN06G2784' => 'fan', 'FAN08G2651' => 'fan', 'FAN10G4238' => 'fan', 'FAN11G1882' => 'fan', 'FAN13G1003' => 'fan', 'FAN14G5429' => 'fan', 'FAN16G0104' => 'fan', 'FAN18G0438' => 'fan', 'FAN18G4450' => 'fan', 'FAN21G2189' => 'fan', 'FAN25G0871' => 'fan', 'FAN28G0010' => 'fan', 'FvH4_3g44850' => 'fve', 'FvH4_5g12310' => 'fve', 'FvH4_7g00060' => 'fve', 'Glyma.05G154600' => 'gma', 'Glyma.07G090600' => 'gma', 'Glyma.08G112300' => 'gma', 'Glyma.08G232500' => 'gma', 'Glyma.11G256100' => 'gma', 'Glyma.16G182800' => 'gma', 'Glyma.16G183100' => 'gma', 'Glyma.16G184100' => 'gma', 'Glyma.16G184600' => 'gma', 'Glyma.16G186325' => 'gma', 'Glyma.16G187851' => 'gma', 'Glyma.16G188200' => 'gma', 'Glyma.16G188575' => 'gma', 'Glyma.16G188800' => 'gma', 'Glyma.16G191201' => 'gma', 'Glyma.16G191666' => 'gma', 'Glyma.16G193400' => 'gma', 'Glyma.16G193800' => 'gma', 'Glyma.U006701' => 'gma', 'Glyma.U006900' => 'gma', 'Glyma.U044300' => 'gma', 'Glyma.U044700' => 'gma', 'Gohir.A05G000700' => 'ghi', 'Gohir.A06G102700' => 'ghi', 'Gohir.A08G011600' => 'ghi', 'Gohir.A08G026640' => 'ghi', 'Gohir.A08G079600' => 'ghi', 'Gohir.A08G094548' => 'ghi', 'Gohir.D05G001000' => 'ghi', 'Gohir.D06G111700' => 'ghi', 'Gohir.D07G003700' => 'ghi', 'Gohir.D08G022100' => 'ghi', 'Gohir.D08G037101' => 'ghi', 'Gohir.D08G089200' => 'ghi', 'Gohir.D08G106000' => 'ghi', 'Gorai.004G017400' => 'gra', 'Gorai.004G035100' => 'gra', 'Gorai.004G094000' => 'gra', 'Gorai.004G112700' => 'gra', 'Gorai.009G000900' => 'gra', 'Gorai.010G127100' => 'gra', 'GSVIVG01001350001' => 'vvi', 'GSVIVG01008272001' => 'vvi', 'GSVIVG01015444001' => 'vvi', 'GSVIVG01025408001' => 'vvi', 'GSVIVG01025413001' => 'vvi', 'HanXRQChr04g0117421' => 'han', 'HanXRQChr07g0196741' => 'han', 'HanXRQChr13g0405111' => 'han', 'Haze_03275' => 'cav', 'Haze_18658' => 'cav', 'Haze_22982' => 'cav', 'Hma1.2p1_0018F.1_g013130' => 'hma', 'Hma1.2p1_0128F.1_g059840' => 'hma', 'Hma1.2p1_0963F.1_g241950' => 'hma', 'Hma1.2p1_2088F.1_g313820' => 'hma', 'HPP92_009602' => 'vpl', 'HPP92_009603' => 'vpl', 'HPP92_017556' => 'vpl', 'HPP92_024366' => 'vpl', 'Hund07574' => 'sun', 'Hund21644' => 'sun', 'Hund24821' => 'sun', 'Lalb_Chr01g0009351' => 'lal', 'Lalb_Chr03g0031991' => 'lal', 'Lalb_Chr07g0186701' => 'lal', 'Lalb_Chr11g0075961' => 'lal', 'Lalb_Chr12g0205391' => 'lal', 'Lalb_Chr13g0294921' => 'lal', 'Lalb_Chr22g0353021' => 'lal', 'Lj1P459T0' => 'lonja', 'Lj2g0016430' => 'lja', 'Lj2P716T7' => 'lonja', 'Lj3g0004263' => 'lja', 'Lj3g0011561' => 'lja', 'Lj3g0019329' => 'lja', 'Lj3g0023144' => 'lja', 'Lj4g0012044' => 'lja', 'Lj6g0015554' => 'lja', 'Lj7A640T28' => 'lonja', 'Lj9P619T29' => 'lonja', 'Lju124C23T8' => 'lonja', 'Lsat_1_v5_gn_2_101621' => 'lsa', 'Lsat_1_v5_gn_6_52380' => 'lsa', 'Lsat_1_v5_gn_6_52460' => 'lsa', 'Lsat_1_v5_gn_7_33800' => 'lsa', 'Lsat_1_v5_gn_9_46221' => 'lsa', 'Manes.03G068100' => 'mes', 'Manes.05G143879' => 'mes', 'Manes.10G152900' => 'mes', 'Manes.15G105800' => 'mes', 'Mapoly0001s0562' => 'mpo', 'Mapoly0033s0039' => 'mpo', 'MBI01_g44283_MAGBIO' => 'mbi', 'MBI04_g09737_MAGBIO' => 'mbi', 'MBI04_g35344_MAGBIO' => 'mbi', 'MBI12_g23293_MAGBIO' => 'mbi', 'MBI12_g26679_MAGBIO' => 'mbi', 'MD02G1320100' => 'mdo', 'MD03G1007900' => 'mdo', 'MD06G1215100' => 'mdo', 'MD07G1000800' => 'mdo', 'MD11G1011100' => 'mdo', 'MD14G1225900' => 'mdo', 'MD15G1181100' => 'mdo', 'Medtr1g041595' => 'mtr', 'Medtr1g042750' => 'mtr', 'Medtr3g083760' => 'mtr', 'Medtr6g084630' => 'mtr', 'Medtr7g014880' => 'mtr', 'Medtr8g085560' => 'mtr', 'Medtr8g446830' => 'mtr', 'MELO3C014672.2' => 'cme', 'MELO3C015638.2' => 'cme', 'MELO3C017299.2' => 'cme', 'MELO3C023502.2' => 'cme', 'Migut.B01405' => 'egut', 'Migut.D02530' => 'egut', 'Migut.K00716' => 'egut', 'Migut.N00574' => 'egut', 'MSTRG.12784' => 'ama', 'MSTRG.17074' => 'ama', 'MSTRG.18006' => 'ama', 'MSTRG.18862' => 'ama', 'MSTRG.20950' => 'ama', 'MSTRG.28104' => 'ama', 'MSTRG.6493' => 'ama', 'Nitab4.5_0000009g0110' => 'nta', 'Nitab4.5_0000468g0150' => 'nta', 'Nitab4.5_0000582g0250' => 'nta', 'Nitab4.5_0000775g0090' => 'nta', 'Nitab4.5_0001059g0030' => 'nta', 'Nitab4.5_0001599g0040' => 'nta', 'Nitab4.5_0002939g0020' => 'nta', 'Nitab4.5_0004212g0020' => 'nta', 'Nitab4.5_0004412g0080' => 'nta', 'Nitab4.5_0004502g0030' => 'nta', 'Nn2g15782' => 'nnu', 'Nn4g23809' => 'nnu', 'Nn7g35928' => 'nnu', 'Oeu018252.2' => 'oeu', 'Oeu033930.1' => 'oeu', 'Oeu033931.1' => 'oeu', 'Oeu034270.1' => 'oeu', 'Oeu040303.1' => 'oeu', 'Oeu041510.1' => 'oeu', 'Oeu058027.1' => 'oeu', 'Os03g0167000' => 'osa', 'Os03g0804200' => 'osa', 'Os07g0198300' => 'osa', 'Peaxi162Scf00015g00837' => 'pax', 'Peaxi162Scf00100g00081' => 'pax', 'Peaxi162Scf00258g00928' => 'pax', 'Peaxi162Scf00402g00931' => 'pax', 'Peaxi162Scf00552g00310' => 'pax', 'PGR031G2307' => 'pgr', 'PGR083G0397' => 'pgr', 'PGR102G1670' => 'pgr', 'PGR102G2431' => 'pgr', 'PGSC0003DMG400005630' => 'stu', 'PGSC0003DMG400028778' => 'stu', 'PGSC0003DMG400028977' => 'stu', 'PGSC0003DMG400032182' => 'stu', 'Phvul.001G268300' => 'pvu', 'Phvul.002G234400' => 'pvu', 'Phvul.004G115800' => 'pvu', 'Phvul.004G115900' => 'pvu', 'Phvul.004G158600' => 'pvu', 'Phvul.011G181000' => 'pvu', 'Potri.001G008500' => 'ptr', 'Potri.001G232000' => 'ptr', 'Potri.003G217000' => 'ptr', 'Potri.006G195700' => 'ptr', 'Potri.015G053700' => 'ptr', 'Potri.015G054000' => 'ptr', 'Pp3c19_17730' => 'ppa', 'Pp3c1_31020' => 'ppa', 'Pp3c2_6280' => 'ppa', 'Prupe.2G001800' => 'ppe', 'Prupe.5G220400' => 'ppe', 'Prupe.6G009900' => 'ppe', 'Prupe.7G234500' => 'ppe', 'Psat1g038200' => 'psa', 'Psat4g142560' => 'psa', 'Psat5g103120' => 'psa', 'Psat7g073960' => 'psa', 'PSO017G3383' => 'pso', 'PSO063G1865' => 'pso', 'PSO063G3660' => 'pso', 'PSO063G6263' => 'pso', 'PSO063G7017' => 'pso', 'PSO063G7434' => 'pso', 'PSO339G0664' => 'pso', 'PSO339G5879' => 'pso', 'PSO384G1652' => 'pso', 'PSO478G4011' => 'pso', 'PSO782G1924' => 'pso', 'PSO832G2291' => 'pso', 'PSO832G3665' => 'pso', 'PSO832G3989' => 'pso', 'PSO832G4036' => 'pso', 'PSO832G4486' => 'pso', 'QL01p008012' => 'qlo', 'QL04p001328' => 'qlo', 'QL04p001667' => 'qlo', 'QL04p001867' => 'qlo', 'QL10p025070' => 'qlo', 'RcHm_v2.0_Chr1g0313181' => 'rch', 'RcHm_v2.0_Chr5g0081561' => 'rch', 'RcHm_v2.0_Chr7g0185251' => 'rch', 'Rhsim01G0091200' => 'rsi', 'Rhsim03G0004300' => 'rsi', 'Rhsim07G0049400' => 'rsi', 'Rhsim13G0208600' => 'rsi', 'Rhsim13G0230400' => 'rsi', 'Sabra01G0006600' => 'sbr', 'Sabra03G0162100' => 'sbr', 'Sabra06G0150400' => 'sbr', 'Sabra15G0075400' => 'sbr', 'Sabra16G0138800' => 'sbr', 'SalBow3G2808' => 'sbo', 'SalBow4G0134' => 'sbo', 'SalBow4G0146' => 'sbo', 'SalBow5G2557' => 'sbo', 'SalBow6G2319' => 'sbo', 'Sc09g0000250' => 'sci', 'Sc12g0006800' => 'sci', 'Sc19g0006090' => 'sci', 'Sc20g0003810' => 'sci', 'Sed0004540' => 'sed', 'Sed0015787' => 'sed', 'Sed0019444' => 'sed', 'Sed0023138' => 'sed', 'SEGI_09836' => 'sgi', 'SEGI_17852' => 'sgi', 'SEGI_19364' => 'sgi', 'SEGI_40266' => 'sgi', 'SEGI_40962' => 'sgi', 'SGA_v2.0_scaffold25G10987' => 'sas', 'SGA_v2.0_scaffold3G01655' => 'sas', 'SGA_v2.0_scaffold6G03428' => 'sas', 'SGA_v2.0_scaffold95G28767' => 'sas', 'SMO112G0091' => 'smo', 'SMO166G0001' => 'smo', 'SMO304G0142' => 'smo', 'SMO364G0558' => 'smo', 'Solyc01g005985.1' => 'sly', 'Solyc01g073680.4' => 'sly', 'Solyc03g119620.1' => 'sly', 'Solyc06g069110.4' => 'sly', 'Sopen01g002000' => 'spe', 'Sopen01g033240' => 'spe', 'Sopen03g038450' => 'spe', 'Sopen06g026390' => 'spe', 'Sp1g40920' => 'spa', 'Sp4g26360' => 'spa', 'Sp4g26370' => 'spa', 'Sp5g04330' => 'spa', 'Sp5g29100' => 'spa', 'TAR369G0318' => 'tar', 'TAR374G0983' => 'tar', 'TAR622G0486' => 'tar', 'TAR623G0881' => 'tar', 'TAR627G0349' => 'tar', 'TAR633G0401' => 'tar', 'TAR633G1632' => 'tar', 'THA.LOC104810336' => 'tha', 'THA.LOC104813902' => 'tha', 'THA.LOC104815116' => 'tha', 'THA.LOC104815658' => 'tha', 'THA.LOC104817145' => 'tha', 'THA.LOC104824489' => 'tha', 'Thecc.01G416800' => 'tca', 'Thecc.03G033700' => 'tca', 'Thecc.05G177900' => 'tca', 'Thecc.09G115800' => 'tca', 'Thecc.09G212300' => 'tca', 'Thhalv10001634m.g' => 'esa', 'Thhalv10001638m.g' => 'esa', 'Thhalv10006273m.g' => 'esa', 'Thhalv10009608m.g' => 'esa', 'Thhalv10011802m.g' => 'esa', 'Thhalv10019767m.g' => 'esa', 'TPR.G11805' => 'tpr', 'TPR.G22752' => 'tpr', 'TPR.G27880' => 'tpr', 'TPR.G35230' => 'tpr', 'TWI09G1507' => 'twi', 'TWI32G0741' => 'twi', 'TWI60G0572' => 'twi', 'TWI60G1209' => 'twi', 'TWI63G1629' => 'twi', 'TWI81G0158' => 'twi', 'unitig_0.g1212' => 'ugi', 'unitig_0.g366' => 'ugi', 'unitig_699.g19749' => 'ugi', 'vmacro04216' => 'vma', 'vmacro07888' => 'vma', 'vmacro13605' => 'vma', 'vmacro20674' => 'vma', 'vmacro22465' => 'vma', 'vmacro22466' => 'vma', 'VMungo0251G0950' => 'vmu', 'VMungo0464G0436' => 'vmu', 'VMungo1383G2079' => 'vmu', 'Zm00001eb005130' => 'zma', 'Zm00001eb061400' => 'zma', 'Zm00001eb302760' => 'zma' ) $gf_id = 'HOM05D001204' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001204' ) $data_identifier = 'HOM05D001204' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 8, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 14, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 22, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 16, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 6, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb302760' $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